| Variant ID: vg0234823331 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34823331 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 313. )
TTGTGAACTTAACGCATAGCTGGCGCTGGATCTCTCTCACCGGCAGCTCCAGGTTGTTGAACTATATGCCCCTTCCTTTCCTCTGCGAAGTTTTCCATTT[C/T]
GCAAAATTTGCAAAGCATTTATACTCTTGTGCTTTCTGTGGTACATGAAATTGCCATATTGTAACTTTGGTGGAGTATGTGTTGTGATGATAGATGAAAT
ATTTCATCTATCATCACAACACATACTCCACCAAAGTTACAATATGGCAATTTCATGTACCACAGAAAGCACAAGAGTATAAATGCTTTGCAAATTTTGC[G/A]
AAATGGAAAACTTCGCAGAGGAAAGGAAGGGGCATATAGTTCAACAACCTGGAGCTGCCGGTGAGAGAGATCCAGCGCCAGCTATGCGTTAAGTTCACAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.00% | 8.90% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 72.80% | 27.20% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 74.80% | 25.20% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 76.20% | 23.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 58.90% | 40.70% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 8.90% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234823331 | C -> T | LOC_Os02g56810.1 | downstream_gene_variant ; 3562.0bp to feature; MODIFIER | silent_mutation | Average:48.135; most accessible tissue: Callus, score: 63.346 | N | N | N | N |
| vg0234823331 | C -> T | LOC_Os02g56820.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.135; most accessible tissue: Callus, score: 63.346 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0234823331 | NA | 2.94E-08 | mr1691_2 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0234823331 | NA | 1.21E-06 | mr1754_2 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0234823331 | 3.73E-06 | 3.73E-06 | mr1754_2 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |